Apple Stores get shipments everyday, except Sundays. Yes, even when every where is sold out. (How else do you expect them to replenish supply?) However, they don't usually know what's in those shipments until they open them.
It's always been my experience that Apple Stores seem better, and more regularly stocked than AT&T or Best Buy. Best suggestion I have for you is to call around to the Apple Stores. As you know, there are several in the Bay Area, including on Stockton and Chestnut, in Stonestown, then two in Palo Alto, and another in Emeryville. The Stockton Street flagship store had iPhones at least through Saturday during release weekend, and I saw a woman purchasing an iPhone 4 from the same store on Monday or Tuesday of this week.
Call ahead. You'll probably be put on hold, but the Apple Store staff should be able to give you a more up-to-date inventory than us on Macrumors.